Nucleosides and Oligonucleotides for Studies on Reversal of Cytotoxic and Mutagenic Damage of DNA and as Diagnostics Tools

ABSTRACT

The present invention is directed to n-alkylated synthetic nucleosides of high regiospecific purity and oligonucleotides that can be utilized for studies on reversal of cytotoxic and mutagenic DNA damage, and as diagnostic tools.

CROSS REFERENCE TO OTHER APPLICATION

This application is a continuation application to U.S. application Ser.No. 14/185,907, filed Feb. 20, 2014, which in turn is a continuationapplication to U.S. application Ser. No. 11/018,567, now U.S. Pat. No.8,785,619, filed Dec. 20, 2004, which in turn claims priority to U.S.Provisional Application Ser. No. 60/531,237, filed Dec. 20, 2003. Theentire teachings of the above applications are incorporated herein byreference.

FIELD OF THE INVENTION

This invention relates to n-alkylated synthetic nucleosides andphosphoramidites of high regio-specific purity and stability andselective deprotection for high purity n-alkylated DNA and RNA synthesisuseful for study of mechanism of cytotoxic and mutagenic DNA damage thatoccurs from the incorporation of methylated nucleosides, thecorresponding phosphates and triphosphates and their precursors, via denovo DNA synthesis. The phosphoramidites of the synthetic alkylatednucleosides have been developed to synthesize sequence specificoligonucleotides and subsequent studies on reversal of cellularcytotoxic and mutagenic damages, in terms of presence of in vivocapability to detect the cellular capabilities for reversal of potentialmutagenic and cytotoxic damages. The reagents thus could be extremelyvaluable tools as diagnostics reagents for cellular capability ofreversal of cellular mutagenic and cytotoxic damages.

BACKGROUND OF THE INVENTION

Alkylation of DNA presents an important event of far reaching biologicalconsequences. DNA alkylating agents are present endogenously, found inthe environment, and are used in chemotherapy. Human beings areconstantly exposed to alkylating agents from a wide variety of sources.For a better understanding of the changes at gene level responsible forDNA damage and a timely intervention in the DNA damaging process,availability of critical nucleosides, DNA and RNA to study the mechanismof DNA damage and repair is required. The information thus generatedwould have vast implication on understanding of various diseases thatare the direct result of DNA damage from alkylation. Since all thealkylation and resulting mutation involve changes at gene level, thecontrol of such damages at the gene level is an ideal approach.

Efforts are needed towards identification of alkylating agents,development of nucleosides and oligonucleotides which are suitable tosynthesize alkylated DNA and RNA oligonucleotides, valuable in the studyof optimum structural parameters for the reversal of cytotoxic DNA andRNA produced endogenously. This is essential, since application of thereversal process at early stages when mutation is at the beginning stagewill help effective control of lesions that are at benign stages oftoxic development.

The two main places of alkylation of DNA are O-alkylation andN-alkylation. Alkylation of DNA may lead to cytotoxic and mutagenicdamage of the gene and gene products. However, the extent of damagedepends upon the site of alkylation as well as on the nature of thebase. N-Methylation of guanine occurs mainly at N⁷ position. However,this alkylation does not interfere with its pairing with cytosine and istherefore, harmless. The glycosidic bond of N⁷-methyl G undergoes slowand spontaneous hydrolysis creating a apurinic site which is a targetfor repair. On the other hand, N⁷-alkylation of G with a bifunctionalagent such as nitrogen mustard causes cross-linking of two neighboringguanines leading to cell toxicity.

In the mono alkylation of adenine, the alkyl group at N³ occupies minorgrove of the DNA double helix causing interference to DNA polymeraseactivity thus resulting in a major toxic lesion.

3-Alkyl guanines behave in a similar fashion as 3-alkyl adenines.However, formation of 3-alkyl guanines is much less prevalent (˜10 foldless) and therefore, of lesser significance. N¹-alkylation of adenineinterferes with A-T pairing. However, this lesion gets slowly excised invivo.

O-Alkylation of the DNA bass fixes them in their enolic forms that mayinfluence their base pairing. Thus, O6-methyl guanine forms an O⁶ Me G-Cbase pair that is more stable in a DNA duplex than O6-Me G-T basemispair. However, DNA polymerase activity shows preference forincorporation of Ton replication. The enolic forms of O⁴-methyl thymineand O4-ethyl thymine form base mispair with G that undergoes replicationof a defined DNA sequence. However, alkyl pyrimidines are very minorproducts of DNA alkylation and are therefore, of low significancetowards biological effects.

O-Alkylation of the phosphate residue in DNA results in the formation ofa triester. Such triesters are repairable and do not seem to beimportant in inducing cell toxicity or mutagenic activity.

Therefore, from the above discussion it is clear that alkylation of DNAmay cause cytotoxic and mutagenic damage depending upon the site ofalkylation. This may have serious consequences in the formation of Geneand Gene products. In nature human beings are constantly exposed toalkylating agents from a wide variety of sources as mentioned above.Repair of the damaged DNA is therefore essential for normal activity.All living cells possess various DNA repair enzymes. These are morepredominant in humans as compared to rodents. Under the influence ofalkylating agents, E. coli respond by inducing the expression of fourgenes, ada, alkA, aidB, and alkB. The ada protein is an O⁶-methylguanine-DNA methyltransferase and also regulates this adaptive response.AlkA is a 3-methyl adenine-DNA glycosylase, and aidB is meant to destroycertain alkylating agents. AlkB was isolated in 1983 by Kataoka et. al(Kataoka, H, Yamamoto, Y, & Sekiguchi, M., J. Bacteriol. 153, 1301-1307,1983) but its exact role is still not clear. It has been shown toprotect human cells against alkylation induced toxicity (Chen, B. J.,Carroll, P., & Sanson, L., J. Bacteriol 176, 6255-6261, 1994). Itprocesses the cytotoxic DNA damage generated in single-stranded DNA bySN2 methylating agents such as Mel, dimethylsulphate, methylmethanesulphonate etc. (Dinglay, S., Trewick, S. C., Lindahl, T., &Sedgwick, B., Genes Dev 14, 2097-2105, 2000). Its role in oxidativedemethylation identified recently, is discussed under direct reversal ofalkylated DNA. In a recent study it has been demonstrated that AlkBsuppresses both genotoxicity and Mutagenesis at low doses of1-alkylpurine and 3-alkylpyrimidine DNA damages in vivo (J. C. Delanyand J. M. Essigmann, PNAS, USA, 101, 39, 14051-14056, 2004). Similarlyit has been shown that N³-methylthymidine containing oligonucleotidescould be repaired by AlkB in vitro (P. Koivisto, P. Robins, T. Lindahl,B. Sidgwick, J. Biol. Chem., 10, 1074, 2004).

There are two types of DNA repair mechanisms that operate in livingcells: i) excision repair of altered residues and ii) direct reversal ofmodified DNA.

Excision repair is the most common mechanism that operates in mammaliancells for DNA repair. There are two types of excision repair: a)nucleotide excision and b) base excision. Both are error freemechanisms. In the nucleotide excision repair, an endonuclease initiatesthe process by making an excision on the single strand on either side ofthe lesion of the damaged nucleotide some 12 base apart. The excisednucleotide containing the lesion is released by DNA helicase B while itis still bound to the protein complex. The gap thus created on thesingle strand is filled up by DNA polymerase I that binds and fills thegap and subsequently the ligation is completed.

In base excision, the enzyme DNA glycosylase hydrolyses the glycosidicbond of modified purine or pyrimidine nucleosides. Thus, the enzyme3-methyl adenine-DNA glycosylase acts on 3-methyl adenine. The next stepis incision of the phosphate backbone by an AP endonuclease followed byexonuclease action which excises the nucleoside creating a gap on thesingle strand. Filling of the gap by DNA polymerase I followed byligation as mentioned for nucleotide excision process, completes therepair process.

Direct reversal of damaged DNA also occurs under the influence ofcertain enzymes. Thus, O-demethylation in O⁶-methyl guanine is effectedby the enzyme O6-methylguanine DNA methyltransferase. The SH group ofPro-Cys-His sequence of the enzyme near its C terminus, acts as a methylacceptor, thus converting O-Me to OH. The same enzyme can alsodealkylate ethyl, 2-hydroxyethyl, and 2-chloroethyl O⁶-derivatives ofguanine.

N-dealkylation is effected by alkB protein. Recently it has been shownby two independent groups (Faines, P. O., Johanson, R. F., & Seeberg,E., Nature, 419, 178, 2002; Trewick, S. C., Henshaw, T. F., Hausinger,R. P., Lindahl, T., & Sedgwick, B., Nature, 419, 174-178, 2002) thatalkB resembles the Fe(ll)- and α-ketoglutarate-dependent dioxygenase.The enzyme couples oxidative decarboxylation of α-ketoglutarate to thehydroxylation of methylated bases in DNA, resulting in the reversal tounmodified base and release of formaldehyde as shown below:

Modified nucleosides and nucleotides find application in variouschemical and biological studies. Such modifications have been linked tocontrol of gene expression at both the levels of transcription andtranslation. For these studies, purified preparations of alkylatednucleosides and nucleotides are required. A large number of N-methylpurines have been isolated from various biological sources andidentified (Jones, J. W., Robins, R. K., J. Am. Chem. Soc, 84, 1914,1962).

Alkylation of various unprotected derivatives of guanine led to amixture of products. alkylated at N¹, N, N⁷, or O⁶ positions (Kamimura,T., Tsuchiya, M., Urakani, K. 1., Kaura, K., Sekine, M., J. Am. Chem.Soc. 106, 4552-4557, 1984).

Extensive work has also been reported on synthetic approach to alkylatednucleosides and nucleotides. Bredreck and Martini (Bredereck, H., andMartini, A., Ber, 80, 401, 1948) treated triacetyl guanosine with excessdiazomethane to obtain 1-methyl guanosine. However, the product waslater shown to be 7-methyl guanosine (Jones, J. W., and Robins, R. K.,J. Am. Chem. Soc. 85, 193-201, 1963). Methylation at pH 13-14 withdimethylsulphate in the presence of alkali gave a mixture of 7-methylguanosine with methylation occurring at ribose unit as well.O⁶-Alkylation of guanosine has also been reported (Ramaswamy, K. S.,Bakir, F., Baker, B., Cook, P. D., J. Heterocycl. Chem. 30, 1373-1378,1993). Regioselective alkylation at N¹ position of guanosine wasachieved by Vincent et. al (Vincent, S. P., Mioskowski, C., and Lebeau,L., Nucleosides and Nucleotides, 18, 2127-2139, 1999).

Methylation of adenosine, 2′-deoxyadenosine, 2′-deoxyguanosine, inosineand xanthosine have been reported by Jones and Robins (Jones, J. W., andRobins, R. K., J. Am. Chem. Soc. 85, 193-201, 1963).

It has been found that the above mentioned alkylated derivatives undergofacile transformation such as Dimroth rearrangement, in which the methylgroup is transferred from one nitrogen to a neighboring one. Thus, ithas been reported that N¹-methyl-2′-deoxyadenosine undergoes conversioninto N⁶-methyl-2′-deoxyadenosine in 25% aq. ammonia with a half life of36 hrs. In another study it was found that N¹-methyl adenosine wasstable for 3 days in 2M methanolic ammonia at room temperature and in 6days time was totally converted into N⁶-methyl adenosine (Mikhailov, S.N., Rozensski, J., Efimtseva, E. V., Busson, R., Aershot, A. V., andHerdewijn, P., Nucleic Acid Res 30, 1124-1131, 2002; Maca, J. B., andWolfender R., Biochemistry, 38, 13338-13346, 1968; Jones, J. W. andRobins, R. K., J. Am. Chem Soc, 85, 193-201, 1963). We found substantialmigration of methyl group from N¹ to N⁶ in the presence of 2M methanolicammonia.

This instability of the molecule prevents their use for development ofalkylated nucleosides and nucleotides.

Incorporation of N1-methyl adenosine into synthetic RNA oligonucleotideshas been recently carried out in which the base moiety of N1-methyladenosine was protected with chloroacetyl group at N6 position(Mikhailov, S. N., Rozensski, J., Efimtseva, E. V., Busson, R.,Aerschot, A. V., and Herdewijn, P., Nucleic Acid Res 30, 1124-1131,2002); subsequently, use of the same protecting group i.e. chloroacetyl,was reported for the preparation ofN6-chloroacetyl-N1-methyl-riboadenosine by the same group (Efimtseva, E.V., Mikhailov S. N., Rozenski, J., Busson, van Aerschot, R. A. andHerdewijn., P. Poster No. P-156, 15th International Round TableConference, Nucleosides, Nucleotides and Nucleic Acids, 10-14 September,2002, Leuven, Belgium.

Efimtseva et al. also reported in the above mentioned Conference thatthe presence of N¹-methyl adenosine in RNA destabilizes a duplex of RNA.

In order to study the effect of enzymes on dealkylation, it is importantto synthesize well characterized alkylated nucleosides and nucleotides.Further, it has been observed that the introduction of a modifiedchloroacetyl protected base improves stability of a hairpin loop in RNA.Since these are important biochemical properties and bear strongimplication of structure, function studies, it is important to ensurethat correct and desired DNA and RNA are synthesized which are free fromimpurities, the side reaction products. Thus, development of nucleosideswith specific protecting groups that prevent migration of the alkylsubstituent in nucleosides during synthesis of desired oligonucleotidesand oligodeoxynucleotides, has been carried out which forms the basis ofthe present invention.

Prior to utilize the N6 chloroacetyl protectedN-1methyl-2′-deoxyadenosine 3′-cyanoethyl phosphoramidite, we carriedout a number of kinetic studies for the deprotection of chloroacetylgroup and determination of presence of any N-6 methyl-2′-deoxyadenosine, Dimroth rearrangement product, and surprisingly we observedN-6 methyl-2′-deoxy adenosine formation to the extent of 8-10%. Oursubsequent studies to develop a ideal group which would be cleanlyremoved under aq. ammonia deprotection condition and would havenegligible amount of Dimroth rearrangement product as bye product. N-6FMOC N-1 methyl-2′-deoxy adenosine-5′-DMT-3′-cyanoethylphosphoramiditeemerged as best reagent with aq. ammonia deprotection taking place verycleanly, and the presence of N-6 methyl-2′-deoxy adenosine was found tobe less than 1%.

SUMMARY OF THE INVENTION

This invention relates to preparation of synthetic nucleosides as usefulsubstrate for oxidative dealkylation studies in relation to reversal ofcytotoxic and mutagenic DNA damage. The synthetic nucleosides areN-alkylated pyrimidines and purines with appropriate nucleobase andsugar protection and the corresponding phosphoramidites, which alsopermit preparation of N-alkylated oligonucleotides andoligodeoxynucleotides for the study of reversal of DNA base mutagenesis.

The present invention aims at appropriately protected nucleosides andoligonucleotides that can be selectively N-alkylated to producecorresponding n-alkylated nucleosides which could be converted intophosphoramidites. The N1-alkylated purine and N-3 alkylated pyrimidineswith appropriate nucleobase amino protection and 5′-DMT protection wereconverted back to nucleobase n-deprotected nucleosides using milddeprotection conditions, and determined to be pure N-alkylated-5′-DMTnucleosides without amino protecting group. Subsequent to this study,the novel N-alkylated-5′-DMT-n-protected nucleoside 3′-phosphoramiditeswere synthesized, which produce defined sequence oligonucleotides. Withsuch types of monomers, the synthetic fully protected oligonucleotidesand oligodeoxynucleotides can then be deprotected under specificdeprotection conditions, without migration of the alkyl substituent.Such oligonucleotides having n-alkylated bases at defined position canserve as reagents for study of reversal of cytotoxic and mutagenicdamage of DNA. Accordingly, the present invention relates to thepreparation of novel pyrimidine and purine nucleosides anddeoxynucleosides of Formula I, Formula 2 and Formula III.

Protected-(N-Alkylated Nucleoside)-OR′   Formula I

wherein, the n-alkylated base is a methylated, ethylated, higher homologof natural or modified DNA base, the sugar residue could be a naturalribose, a deoxyribose or a derivative thereof, OR′ could represents H, aprotecting group, a phosphate bond (P(═O)(OH)2 or a phosphoramidite(P—N″R′″—CH2CH2CN); (P—NR″R″″—OR″″), at 3′ or 5′-position of the sugarunit and specifically include compounds of Formula II to VIII.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. N³-Ethyl-5′-O-DMT-N⁴-Bz-2′-deoxycytidine, UV spectrum graph.

FIG. 2. N³-Ethyl-5′-O-DMT-N⁴-Bz-2′-deoxycytidine, HPLC tracing.

FIG. 3.N³-Ethyl-5′-O-DMT-N⁴-Bz-2′-deoxycytidine-3′-cyanoethylPhosphoramidite,HPLC tracing.

FIG. 4.N³-Ethyl-5′-O-DMT-N⁴-Bz-2′-deoxycytidine-3′-cyanoethylphosphoramidite,UV spectral graph.

FIG. 5. 5′-O-DMT-N⁶-PAC-N¹-Methyl-Deoxyadenosine, HPLC tracing.

FIG. 6.5′-O-DMT-N⁶-PAC-N¹-Methyl-Deoxyadenosine-3′-cyanoethylphosphoramidite;HPLC tracing.

FIG. 7. 5′-O-DMT-N¹-methyl-N⁶-FMOC-2′-deoxyadenosine; Kinetic Test forFMOC Deprotection (20% methanolic ammonia at 37 C. Note: The N⁶-methylmigration product is seen 2.27% after complete deprotection).

FIG. 8. HPLC Coinjection of 5′-O-DMT-N¹methyl-2′-deoxyadenosine and5′-O-DMT-N⁶-methyl-2′-deoxyadenosine. Note: The retention timedifference of 0.553 minutes is observed. The N¹ methyl compound elutesslightly faster.

FIG. 9. N¹-Methyl-N²-DMF-Deoxyguanosine; UV Spectral graph.

FIG. 10. N¹-Methyl-N²-DMF-Deoxyguanosine; HPLC data.

FIG. 11. 5′-O-DMT-N¹-Methyl-N²-DMF-Deoxyguanosine; UV Spectral graph.

FIG. 12. 5′-O-DMT-N¹-Methyl-N²-DMF-Deoxyguanosine; HPLC data.

FIG. 13.5′-O-DMT-N¹-Methyl-N²-DMF-Deoxyguanosine-cyanoethylphosphoramidite; UVSpectral graph.

FIG. 14.5′-O-DMT-N¹-Methyl-N²-DMF-Deoxyguanosine-cyanoethylphosphoramidite; HPLCdata.

DETAILED DESCRIPTION OF THE INVENTION

This invention relates to compounds of Formula 1 which specificallyincludes compounds represented by Formulae II to IX;

Formula II is

Formula III is

wherein, R₁ is an alkyl such as methyl, ethyl, X is H, a lower alkylcontaining 1 to 6 carbon atoms, such as CH₃, C₂H₅, n-C₃H₇, etc., abranched chain lower alkyl such as iso-C₃H₇, iso-C₄H₉, t-C₄H₉ etc.,5-aza, halogen (F, Cl, Br, I), propyne, Z is H or OCH₃, F, protected NH₂group, tbdsilyl protecting group, tetrahydropyranyl protecting orlikewise groups. Y could be H, a protecting group such as MMT(monomethoxytrityl), DMT (dimethoxytrityl), TMT (trimethoxytrityl), FMOC(9-fluorenylmethyloxy carbonyl), tetrahydropyranyl, benzoyl,phenoxyacetyl, acetyl, propyl, butyryl, isobutyryl, or other higherhomologs. The common group substitution of benzoyl group could be alkylor halogen groups. The common substitution of phenoxy acetyl group orappropriately protected phenoxyacetyl group could be lower alkyl, loweralkoxy, nitro, halogen (F, Cl, Br, I). The substitution at 3′ position,R′, could be a phosphate residue (—P(═O)(OH)₂), a thio phosphate(—P(═S)(OH)₂), a phosphoramidite such as P—N(R₂,R₃)(OCH₂CH₂CN),P—N(R₂,R₃)(OR₄) wherein R₂, R₃ could be diisopropyl, diethyl, dimethyl,morpholino, pyrrolidino, and R4 is a lower alkyl containing 1-6 carbonatoms such as CH₃, C₂H₅, n-C₃H₇, iso-C₃H₇, t-C₄H₉.

Formula IV is

Formula V is

wherein, R₁ is benzoyl, acetyl, phenoxyacetyl, substituted phenoxyacetylisobutyryl, 9-FMOC, dialkylformamidine and likewise base protectinggroups for n-alkyl cytosine moiety. X, X₁, Z, and Y are as defined inFormula II, III, IV and V. X₁, X₂ could be individually a substituent,same or different, as defined for X. Y and R′ are defined in formula IIand III.

A purine derivative as shown in Formula VI

Formula VII is

wherein, R₁ has been defined in formula IV and V; Y, Z are as defined inFormula II, III, IV and V. R₅ is a protecting group such as, phenoxyacetyl, protected phenoxy acetyl, pivaloyl, 9-FMOC group, an iminederivative such as formamidine, dimethylformamidine. A purinemodification could be, but not limited to, 7-deazaadenine,7-iodo-7-deazaadenine, 7-propyne-7-deaza adenine.

A purine derivative as shown in Formula VIII,

A purine derivative as shown in Formula IX,

wherein, R₁, R₅, are defined in formula VI and VII, Z and Y, are asdefined in Formula II-VII, a purine modification could be, but notlimited to, 7-deazaguanine, 7-iodo-7-deazaguanine,7-propyne-7-deazaguanine.

Preferred Compounds of the invention are:

-   1. N¹-Methyl-N⁶-PAC-deoxyadenosine (1)-   2. 5′-O-DMT-N⁶-PAC-N¹-Methyl-deoxyadenosine (2)-   3. 5′-O-DMT-N⁶-PAC-N¹-Methyl-deoxyadenosine-3′-cyanoethyl    phosphoramidite (3)-   4. N¹-Methyl-N²-DMF-deoxyguanosine (4)-   5. 5′-O-DMT-N¹-Methyl-N²-DMF-deoxyguanosine (5)-   6. 5′-O-DMT-N¹-Methyl-N²-DMF-deoxyguanosine-3′-cyanoethyl    Phosphoramidite (6)-   7. N³-Ethyl-5′-O-DMT-N⁴-Bz-2′-deoxycytidine (7)-   8. N³-Ethyl-5′-O-DMT-N⁴-Bz-2′-deoxycytidine-3′-N,N-diisopropyl    cyanoethyl phosphoramidite (8)-   9. N¹-Methyl-N⁶-FMOC-2′-deoxyadenosine (9)-   10. 5′-DMT-N¹-Methyl-N⁶-FMOC-2′-deoxyadenosine (10)-   11.    5′-DMT-N¹-Methyl-N⁶-FMOC-2′-deoxyadenosine-3′-cyanoethyl,n,n-diisopropyl    phosphoramidite (11).

EXPERIMENTAL EXAMPLES Preparation of N¹-Methyl-N⁶-PhenoxyAcetyl-Deoxyadenosine (1)

N¹-Methyl deoxy adenosine (made by adding methyl iodide in dimethylacetamide solution of dA and stirring at room temp. for 18 hours) (J. W.Jones and R. K. Robins, J. Am. Chern Soc, 85, 193-201, 1963). 18.8 mmolewas taken in dry pyridine 50 ml and the solution was cooled to 0° C. and75.5 mmole trimethyl chloro silane was added dropwise under argon.Reaction mixture was brought to 30° C. and stirred for half an hour.Reaction mixture was cooled to 0° C. and 37.5 mmole phenoxy acetylchloride was added drop wise under argon and stirred at 30° C. for 2.5hours. Reaction was cooled again to 0° C. and 10 ml distilled water wasadded and stirred for 10 minutes then 5 ml pre-cooled ammonium hydroxidesolution (28%) was added at 0° C. and stirred for 2 minutes. Thesolution was then evaporated under high vacuum to gum. The gum was thentaken in chloroform and extracted twice with water. The organic layerwas dried on sodium sulfate and evaporated to gum. TLC of this compoundshowed two major spots, lower spot was found to be the right spot. Theresidue was then purified on silica gel column using chloroform and agradient system containing 5-10% methanol in chloroform. The pureproduct was pooled and dried. The yield was approx. 25%. TLC R_(f) ofcompound 1, 0.45 in chloroform:methanol 92:8, HPLC analysis showedsingle peak 92% R_(t) 5.1 min (90:10 0.1 M TEAA, pH 7.5: acetonitrile;C-18 Reverse phase column, system A: TEAA:triethylammonium acetate). UV(methanol) λ max (nm) 299 (ε 12,928) ratio 250/260; 0.666, 260/280;0.631.

¹H NMR (CD₃OD): 8.31 (s, 2, H2 & H8), 6.76-7.22 (1d & 2m, 5, O—C₆H₅),6.39-6.42 (t, 1, H1′), 4.91 (s, 2, CH₂—O-Phenyl), 4.53-4.55 (m, 1, H3′),4.01-4.03 (m, 1, H4′), 3.70-3.81 (2q, 2, H5′ & H5″), 3.41 (s, 3, N—CH₃),2.41-2.73 (2m, 2, H2′ & H2″)

Preparation of 5′-O-DMT-N⁶-PAC-N¹-Methyl-Deoxyadenosine (2)

Compound 1 (3.75 mmole) was dried with pyridine then taken in 15 mlpyridine, the solution was cooled to 0° C. and to the stirred solution4.5 mmole DMT-CI was added. Reaction mixture was brought to room temp.and stirred for 2 hours. Then reaction was quenched with pre-cooledmethanol at 0° C. The solution was then evaporated under high vacuum togum. The gum was then taken in chloroform and extracted with 5% aqueoussodium bicarbonate solution and then with saturated brine solution. Theorganic layer was dried on sodium sulfate and evaporated to gum. TLC ofthis compound showed one major spot. Compound was then purified onsilica gel column using chloroform and a gradient system containing 2-5%methanol in chloroform. The pure product was pooled and dried. The yieldwas approx. 65%. TLC R_(f) of compound 2, 0.28 in chloroform-methanol(96:4), HPLC analysis showed single peak 98.3% R_(t) 7.68 min (40:60:0.1 M TEAA:acetonitrile; system B). UV (methanol) λ max nm) 277.5 (ε13,175) ratio 250/260; 1.109, 260/280; 0.616.

¹H NMR (CD₃OD): 8.17 (s, 1, H8), 8.12 (s, 1, H2), 6.73-7.39 (m, 18,aromatic), 6.38-6.41 (t, 1, H1′), 4.90 (s, 2, CH₂—O-Phenyl), 4.58-4.59(m, 1, H3′), 4.13-4.14 (m, 1, H4′), 3.74- 3.75 (ds, 6, OCH₃), 3.39 (s,3, N—CH₃), 3.27-3.37 (2q, 2, H5′ & H5″), 2.47-2.88 (2m, 2, H2′ & H2″).

Preparation of 5′-O-DMT-N⁶-PAC-N¹-Methyl-Deoxyadenosine-3′-cyanoethylphosphoramidite (3)

Compound 2 (1.42 mmole) was thoroughly dried with dry acetonitrile andtaken up in dry tetrahydrofuran. To the stirred solution was addedN,N-diisopropyl ethylamine (2.84 mole) under argon, the solutionmaintained at 5° C. To this solution was added drop wiseN,N-diisopropylamino cyanoethyl phosphoramidic chloride (1.56 mmole),followed by further reaction at 25° C. for additional one hour. Thereaction mixture was diluted with ethyl acetate and washed withsaturated aqueous sodium bicarbonate once, followed by saturated sodiumchloride once. The organic layer was dried over anhydrous sodiumsulfate, followed by evaporation under vacuum. The residue was purifiedby column chromatography. Yield of the pure product was 78%. The solventsystem for column and TLC was ethyl acetate: acetone and triethylaminein a ratio of 90:9:1. The TLC R_(f) of compound 0.5 & 0.59, HPLCanalysis showed sharp doublets 99.2%, R_(t) 3.43 min & 3.69 min(95:5::acetonitrile:0.1 M TEAA; system C), UV(methanol). λ max (nm) 278(ε 12,334) ratio 250/260; 1.099, 260/280; 0.618.

¹H NMR (CDCl₃): 7.87-7.89 (d, 1, H2), 7.74 (s, 1, H8), 6.77-7.43 (m, 18,aromatic), 6.29-6.31 (t, 1, H1′), 4.93 (s, 2, CH₂—O-phenyl), 4.68-4.69(m, 1, H3′), 4.27-4.29 (m, 1, H4′), 3.77-3.83 (m, 1, POCH₂), 3.77 (ds,6, OCH₃), 3.73-3.75 (m, 1, POCH₂), 3.55-3.69 (dm, 2, H5′ & H5″),3.29-3.37 (m, 2, (Me₂CH)₂N), 2.44-2.62 (dt, 2, CH₂CN), 1.15-1.19 (m, 12,[(CH₃)₂C]₂N). ³¹P NMR (CDCl₃) δ 149.392, 149.489, J 0.097.

Preparation of N¹-Methyl-N²-DMF-Deoxyguanosine (4)

N²-DMF-dG (made by regular procedure using dG solution in dimethylformamide and adding dimethyl formamidine dimethyl acetal and continuingthe reaction for 48 hours followed by crystallization) 12.4 mmole wastaken in 40 ml dimethyl formamide. The solution was cooled to 0° C. andthen 13.65 mmole sodium hydride was added under argon and reaction wasstirred for an hour then 13.65 mmole methyl iodide was added at 0° C.and let the reaction proceed at the same temperature for three hours.Reaction became thick solid; 100 ml ether was added and solid wasfiltered through Buchner funnel and washed twice with ether:water(90:10). Solid was dried on high vacuum. The yield was approx. 65%. TLCR_(f) of compound 4, 0.5 in chloroform:methanol 85:15, HPLC analysisshowed single peak 96% R_(t) 1 2.62 min (80:20:: 0.1MTEAA:Acetonitrile:system D). UV (0.2N HCl) λ max (nm) 296 (ε 21,265)ratio 250/260; 1.289, 260/280; 0.412.

¹H NMR (DMSO): 8.56 (s, 1, N═CH—N), 8.04 (s, 1, H8), 6.24-6.26 (t, 1,H1′), 5.30 (s, 1, 5′ OH), 4.92 (s, 1, 3′ OH), 4.37-4.38 (m, 1, H3′),3.81-3.84 (m, 1, H4′), 3.51-3.56 (2q, 2, H5′ & H5″), 3.32 (s, 3, N—CH₃),3.08 & 3.19 (ds, 6, N(CH₃)₂), 2.21-2.24 & 2.5-2.62 (2m, 2, H2′ & H2″).

Preparation of 5′-O-DMT-N1-Methyl-N²-DMF-Deoxyguanosine (5)

Compound 4 (8.3 mmole) was dried with pyridine then taken in 30 ml ofpyridine, the solution was cooled to 0° C. and to the stirred solution10 mmole DMT-Cl was added. Reaction mixture was brought to the roomtemperature and stirred for two hrs. Then reaction was quenched withpre-cooled methanol at 0° C.; the solution was then evaporated underhigh vacuum to gum. The gum was then taken in chloroform and extractedwith 5% aq. sodium bicarbonate solution and then with saturated brinesolution. The organic layer was dried on sodium sulfate and evaporatedto gum. TLC of this compound showed one major spot. Compound was thenpurified on silica gel column using chloroform:hexane:acetone 50:30:20containing 8% methanol. The pure product was pooled and dried. The yieldwas approx. 56%. TLC R_(t) of compound 5, 0.27 inchloroform:hexane:acetone 50:30:20 containing 2% methanol. HPLC analysisshowed single peak 99% R_(t) 4.41 min (system B). UV (methanol) λ max(nm) 307 (ε 17,676) ratio 250/260; 1.678, 260 I 280; 0.584.

¹H NMR (CD₃CN): 8.50 (s, 1, N═CH N), 7.66 (s, 1, H8), 6.77-7.38 (3m, 13,Aroma), 6.26-6.28 (t, 1, H1′), 4.53-4.54 (m, 1, H3′), 3.98 (m, 1, H4′),3.74 (s, 6, OCH₃), 3.55 (s, 3, N—CH₃) 3.17-3.27 (2q, 2, HS' & H5″), 3.10& 3.11 (ds, 6, N(CH₃)₂), 2.34-2.37 & 2.74-2.77 (2m, 2, H2′ & H2″).

Preparation of 5′-O-DMT-N¹-Methyl-N²-DMF-Deoxyguanosine-3′-CyanoethylPhosphoramidite (6)

Compound 5 (3.13 mmole) was thoroughly dried with dry acetonitrile andtaken up in 20 ml dry tetrahydrofuran. To the stirred solution as addedN, N-diisopropyl ethylamine (6.26 mmole) under argon; the solutionmaintained at 5° C. To this solution was added drop wiseN,N-diisopropylamino cyanoethyl phosphoramidic chloride (3.4 mmole),followed by further reaction at 25° C. for additional one hour. Thereaction mixture was diluted with ethyl acetate and washed withsaturated aq. sodium bicarbonate once, followed by saturated sodiumchloride once. The organic layer was dried over anhydrous sodiumsulfate, followed by evaporation under vacuum. The residue was purifiedby column chromatography. Pure fractions were pooled and dried. Yield ofthe pure product was 60%. The solvent system for column and TLC waschloform:hexane and triethylamine in a ratio of 70:20:10. The TLC R_(f)of compound VI, 0.46 & 0.62, HPLC analysis showed sharp doublets 95.5%,R_(t) 3.46 min & 3.53 min (90:10:: acetonitrile:0.1 M TEAA; system E),UV (methanol) λ max (nm) 307 (ε 16,371) ratio 250/260: 1.738; 260/280:0.617.

¹H NMR (CDCl₃): 8.52-8.53 (d, 1, N—CH—N), 7.70-7.71 (d, 1, H8),6.77-7.41 (tm, 13, Ar), 6.36-6.37 (m 1, H1), 4.63-4.71 (m, 1, H3′),4.24-4.25 (m, 1, H4′), 3.77 (ds, 6, OCH₃), 3.57-3.67 (m, 2, H5′ & H5″),3.28-3.32 (m, 4, (Me₂CH)₂N & POCH₂), 3.12-3.18 (dd, 6, N—(CH₃)₂),2.46-2.63 (dm, 4, CH₂CN, H2′, & H2″), 1.15-1.19 (m, 12, ((CH₃)₂C)₂N).³¹P NMR (CDCl₃) δ 149.256-149.392, J 0.136.

Preparation of N³-Ethyl-5′-O-DMT-N⁴-Bz-2′-Deoxycytidine (7)

DMTdBzC (7.0 gm) was taken in dimethylacetamidite (21 ml). To thesolution was added ethyliodide (7.0 ml), stirred for 6 hrs at roomtemperature, and then diisopropylethylamine (1.79 ml) was added. Thesealed reaction mixture was kept at 37° C. for over night and thenpoured in to 10% aq. sodium bicarbonate. The oil was separated, taken inchloroform, and washed with brine and passed through anhydrous sodiumsulfate and evaporated. TLC system was 50:30:20:1(chloform:hexane:acetone:methanol; System F). The crude mixture waspurified by column chromatography on silica gel (70-230 mesh) using asolvent system consisting of dichloromethane:hexane:acetone:: 50:30:20.The title compound (1.4 gm) was obtained in pure form. TLC in system F,R_(f) 0.63. HPLC in 95:5:: acetonitrile:0.1 M TEAA pH 7.5), reversephase, retention time; 2.97 minutes. UV (methanol), ratio 250/260;1.529; 260/280; 0.984; Emax at 250 nm; 13721.

Preparation ofN³-Ethyl-5′-O-DMT-N⁴-Bz-2′-Deoxycytidine-3′-N,N-Diisopropyl CyanoethylPhosphoramidite (8)

To a mixture of N³-ethyl-5′-O-DMT-N⁴-Bz-2′-deoxycytidine (1.0 gm) takenin anhydrous THF (10 ml) and diisopropylethylamine (0.52 ml, 2 eq),N,N-diisopropyl-cyanoethylphosphonamidic chloride reagent (0.37 gm; 1.1eq) was added drop wise at zero degrees. The reaction time was 1 hour.The tic was checked in 60:30:10:: hexane:chloroform:triethylamine. Thereaction mixture was worked up following standard procedure. The crudeproduct was purified on silica gel column (70-230 mesh), column length12 inches, column diameter 1.0 inch. The column chromatography systemwas 30:60:10:: ethyl acetate:hexane:triethylamine. Title compound (600mg) was obtained in pure form with only trace of PV peak. TLC system was30:60:10:: ethyacetate:hexane:triethylamine; R_(f) 0.50. HPLC,(95:5::acetonitrile:0.1 M TEAA pH 7.5); doublet; retention time; 5.51and 5.701, UV (methanol); 250/260; 1.505, 260/280; 0.960, Emax at 250nm; 16343.

Preparation of N¹-Methyl-dA (9)

Reported by J. W. Jones and R. K. Robins, J. Am. Chem. Soc, 85, 193-201,(1963).

2′-Deoxy adenosine (1.0 gm) was taken in dimethylacetamide (3.0 ml),followed by addition of methyliodide (1.0 ml). The reaction mixture wassealed and stirred for 18 hours at room temperature. Deoxyadenosineslowly dissolved and a product slowly precipitated out. After 18 hoursreaction, acetone (15 ml) was added, and stirring continued for 30minutes. The solid was filtered and washed with acetone. TLC was run inseveral systems, (a) Chl:methanol:: 92:8, (b) 75:25:: Chl:methanol (c)in 5% aq. ammonium bicarbonate (d) isopropyl alcohol:ammoniumbicarbonate:: 65:35). A repeat preparation of N¹-Methyl dA, thequantities were dA (10 gm), dimethylacetamidite (30 ml), methyliodide(10 ml). The sealed reaction mixture stirred overnight, followed byaddition of acetone (100 ml). The solid was filtered and washed withadditional acetone. Quantity obtained; 7 gm.

Preparation of N¹-Methyl-N⁶-FMOC-2′-Deoxyadenosine (10)

N¹-Methyl-2′-deoxy adenosine hydroiodide salt (2.5 gm) was taken inpyridine (25 ml). The solution was cooled to 0° C. From pressureequalizing funnel was added chlorotrimethylsilane (2.42 ml; 3 eq) dropwise. The reaction mixture was then brought to room temperature andstirred for 45 minutes at room temperature, followed by addition offluoreriylcarbonyl chloride (FMOC Chloride) (1.96 gm; 1.2 eq) throughpressure equalizing funnel slowly. The reaction mixture was stirred atRT for 2.5 hours. The reaction mixture was brought to zero degrees, andwater (5.0 ml) was added and the mixture stirred for 10 minutes at zerodegrees. This was followed by addition of aq ammonia (3.97 ml), and themixture was stirred for 1.0 minute. The reaction mixture was then pumpedout. TLC run in chloroform:methanol:: 90:10. Column chromatography ofthe above 2.5 gm batch; Column length 14 inches, column diameter 2 inch,solvent system: chloroform-methanol (100 to 90% chloroform gradient)Quantity of pure product obtained; 2.5 gm.

Preparation of 5′-O-DMT-N¹-Methyl-N6-FMOC-2′-Deoxyadenosine3′-Cyanoethylphosphoramidite (11)

To a mixture of 5′-O-DMT-N¹-methyl-N6-FMOC-2′-deoxyadenosine (2;0 gm)taken in anhydrous THF (20 ml) and diisopropylethylamine (0.88 ml, 2eq), N,N-diisopropyl-cyanoethylphosphonamidic chloride reagent (0.62 ml1.1 eq) was added drop wise at zero degrees. The reaction was thenallowed to proceed at room temperature for 1 hour. The tic was checkedin 90:10:1:: ethylacetate:acetone:triethylamine. The reaction mixturewas worked up following standard procedure. The crude product waspurified on silica gel column (70-230 mesh}, column length 12 inches,column diameter 1.5 inches. The column chromatography system was90:10:1:: ethyl acetate:acetone:triethylamine. Title compound (1.6 gm)was obtained in pure form with less than 2% of PV peak. TLC system was90:10:1:: ethylacetate:acetone:triethylamine; R_(f) 0.60. UV (methanol);250/260; 0.757; 260/280; 1.326, Emax; at 266 nm 17408. HPLC (system90:10:: acetonitrile:0.1 M triethylammonium acetate, pH 7.5) retentiontime; 7.31 and 8.18 minutes. ³¹P NMR (CDCl₃); 149.531 and 149.400.

Chemical Studies and Discussion

In the guanine series, position of methyl group on N¹ was confirmed bycomparing with 1H NMR of known sample of N²-Me-dG. It was confirmed byTLC & HPLC that migration of methyl group from N¹ position to N²position of the ring does not take place in the case of Guanosine during24 hours ammonia reaction to knock off N-DMF group.

In the adenine series, it was found that during 20% methanolic ammoniahydrolysis of N-PAC protecting group, approx. 5-6% N¹ methyl migrated toN⁶ position on exocyclic amine in 18 hours at 37 C (required to knockoff Phenoxy acetyl from N⁶ position). To minimize this migration, weintroduced N-FMOC group in place of N-PAC which reduced 20% methanolicammonia hydrolysis time to only 4 hours at 37° C. but even in 4 hours,approx. 2.5% migration took place. This migration of methyl group fromN¹ to N⁶ position was confirmed by TLC & HPLC. The migration ofN-chloroacetyl group as published by was found to be approx. 9-10%.

What is claimed is:
 1. A nucleoside of the formula (II),

wherein, R₁ is methyl; X is hydrogen, a lower alkyl containing 1 to 6carbon atoms, or a branched chain lower alkyl; Y is monomethoxytrityl,dimethoxytrityl, trimethoxytrityl, or tetrahydropyranyl; R′ is aphosphoramidite, said phosphoramidite isP—N(R₂,R₃)(OCH₂CH₂CN) or P—N(R₂,R₃)(OR₄), wherein R₂ and R₃ are selectedfrom the group consisting of diisopropyl, diethyl, dimethyl, morpholino,and pyrrolidino; and R₄ is a lower alkyl containing 1-6 carbon atoms;and Z is hydrogen, fluoro, or protected amino.
 2. A nucleoside of theformula (VIII),

wherein, R₁ is methyl; Y is monomethoxytrityl, dimethoxytrityl,trimethoxytrityl, or tetrahydropyranyl; R′ is a phosphoramidite, saidphosphoramidite isP—N(R₂,R₃)(OCH₂CH₂CN) or P—N(R₂,R₃)(OR₄), wherein R₂ and R₃ are selectedfrom the group consisting of diisopropyl, diethyl, dimethyl, morpholino,and pyrrolidino; and R₄ is a lower alkyl containing 1-6 carbon atoms; Zis hydrogen, fluoro, or protected amino; and R₅ is phenoxy acetyl, paraor ortho chloro phenoxy acetyl, para or ortho nitro phenoxy acetyl, paraor ortho bromo phenoxy acetyl, pivaloyl, 9-fluorenylmethoxycarbonyl(9-FMOC), or a dialkylformamidine.
 3. A method of synthesizing a definedsequence of an oligo-2′-deoxyribonucleotide, comprising the step of:reacting the nucleoside phosphoramidite of one of claim 1 or 2 with anoligo-2′-deoxynucleotide to produce said defined sequence ofoligo-2′-deoxyribonucleotide.
 4. The defined sequence ofoligo-2′-deoxyribonucleotide of claim 3, wherein the nucleoside exhibitsat least 95% regiospecific purity.
 5. An in vitro diagnostic agent forreversal of cytotoxic and mutagenic damage to DNA, comprising: saiddefined sequence of claim 3, wherein the nucleoside phosphoramiditeexhibits at least 95% regiospecific purity.
 6. An in vivo diagnosticagent for reversal of cytotoxic and mutagenic damage to DNA, comprising:said defined sequence of claim 3, wherein the nucleoside phosphoramiditeexhibits at least 95% regiospecific purity.
 7. A process for preparingN3 alkyl-deoxycytidine, said process comprising the steps of: reactingN-4-benzoyl-5′-dimethoxytrityl-2′-deoxycytidine with an alkyl iodide toproduce N-3 alkyl N-4-benzoyl-5′-dimethoxytrityl-2′-deoxycytidine; andconverting N-3 alkyl N-4-benzoyl-5′-dimethoxytrityl-2′-deoxycytidineinto the corresponding phosphoramidite.
 8. The process of claim 7,further comprising the step of: removing protecting groups N-4-benzoyland 5′-dimethoxytrityl from N-3 alkylN-4-benzoyl-5′-dimethoxytrityl-2′-deoxycytidine to produceN-3-alkyl-2′-deoxycytidine.
 9. An oligo-2′-deoxyribonucleotide,comprising at least one of the nucleoside of claims 1 and 2.